Hi, I am interested in comparing peaks from replicates using IDR. I have found that this Galaxy instance has IDR but only provides a genome table for mm9. Is there a Galaxy instance that provides mm10 for IDR? Thanks! Dan
The tool hasn't been updated since 2013, so contacting the tool authors is the best way to learn about other additional available Genome Tables (a built-in index) and upgrade plans (if any).
The tool is installed at https://usegalaxy.org.au and indexed for mm9, not mm10. It is also version 1.0.0 from 2013.
Main Tool Shed (MTS) repository for the tool: https://toolshed.g2.bx.psu.edu/view/modencode-dcc/idr_package/6f6a9fbe264e (includes contact information). If the tool authors upgraded the tool and provided an updated Genome Table, the server you are using or https://usegalaxy.org.au could be contacted to request that the tool be upgraded. Or you could install the upgraded tool into your own Galaxy.
The tool might be available at other public Galaxy servers, but these also probably have same built-in indexes unless they took on independent development (and didn't share the upgrade with the wider community through the MTS). The only way to check is by reviewing the tools on the servers directly as tools installed from the MTS are not tracked. The list of known publically available Galaxy servers is here: https://galaxyproject.org/public-galaxy-servers/. I would suggest starting with those having a ChIP-seq domain focus.
Thanks! Jen, Galaxy team
Thank you for your reply. I went through all the public Galaxy servers and found that https://usegalaxy.org.au is the only Galaxy instance that provides IDR (although a depricated version as I mentioned in my initial post). I have contacted the Modencode and galaxy.org.au administrators to ask if it's possible to update IDR. I am now waiting for them to reply.
I find it quite surprising that no Galaxy server contains an updated version of IDR, given that this tool is now an essential part of the recommended pipeline by Encode/Modencode. I think it would be a greatly beneficial to the community if IDR is installed to main Galaxy instance. Is this something that could be considered by the administrators?
Update: I was informed that galaxy.au will not be installing new tools at the moment. There is a new version of IDR from late 2017 that is wrapped for Galaxy by the IUC team but has not been installed to any Galaxy instance yet. Would the admins of the main Galaxy instance consider installing given its wide benefit to the community?